However, researchers found the chance of having a seizure was still small after the shots, and kids who got them weren't any more likely to go on to develop epilepsy than those who weren't vaccinated, as some evidence had suggested.
The finding is not a reason for parents to avoid the combined vaccine, and is actually "reassuring," said one expert not involved in the study.
According to the National Institutes of Health, about one in every 25 kids will have at least one fever-related seizure -- short-lasting convulsions that don't cause permanent damage. The seizures are especially common in toddlers.
For the new study, researchers tracked about 380,000 babies born in Denmark between 2003 and 2008, through reports their doctors gave to national health registries.
In Denmark, the child vaccination schedule calls for a combined vaccine given at three, five and 12 months of age against diphtheria, tetanus, whooping cough (pertussis), polio and Haemophilus influenzae type 2, known collectively as DTap-IPV-Hib.
Similar vaccine combinations are given in the United States, researchers said.
Previous studies suggested that an older version of the pertussis vaccine caused fevers and increased babies' chances of having a related seizure. But it's been less clear if that risk also applies to newer versions in combined vaccines, according to study author Yuelian Sun, from Aarhus University.
She and her colleagues found that about 7,800 kids, or just over two percent, were diagnosed with a fever-related seizure by the time they were one and a half.
Nine babies had a so-called febrile seizure on the same day as their first combined shot, 12 after the second shot and 27 on the day they got the third shot. That was out of 300,000 to 340,000 kids who had each of the scheduled vaccines.
On the day of the first shot, that risk was about six times higher than would be expected, based on other babies who hadn't recently been vaccinated, and it was four times higher after the second shot.
However, the risk dipped below average a few days after vaccination, and the researchers found that over the week after getting any of their shots, babies weren't more likely to have a febrile seizure than they were during any other week.
Up to seven years after getting their shots, vaccinated kids didn't have any extra risk of being diagnosed with epilepsy, Sun's team reported Tuesday in the Journal of the American Medical Association.
Out of all 300,000-plus kids, including about 7,000 that never received a DTap-IPV-Hib vaccine, just over 2,200 developed epilepsy during the study period.
"The good news of our paper is that we didn't find an increased risk of epilepsy," which is more serious than febrile seizures and may cause brain damage, Sun said.
"The prognosis after febrile seizures is good," she told Reuters Health.
Dr. Eugene Shapiro, a pediatrics and infectious diseases researcher at Yale University in New Haven, pointed out that the absolute risk of having a febrile seizure was still "very small" on the day of vaccinations -- and didn't come with a greater chance of seizure disorders.
"It's not a sign of brain damage," said Shapiro, who wasn't involved in the new research. "It doesn't change your risk of ultimately developing epilepsy."
Sun speculated that babies who had a febrile seizure on the day of their shots could have been more genetically prone to the seizures, and might have had one sooner or later even if they hadn't been vaccinated.
"The other point is, there are children dying of pertussis," Shapiro told Reuters Health, pointing to recent outbreaks of whooping cough in California.
"This is definitely not a reason to not get this vaccine. On the contrary, this should be reassuring."